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Advanced batch computing on the Flux cluster
February 21, 2018 @ 1:00 pm - 5:00 pm
Venue: East Hall B250
Overview
This course will cover some more advanced topics in cluster computing on the U-M Flux Cluster. Topics to be covered include a review of common parallel programming models and basic use of Flux; dependent and array scheduling; advanced troubleshooting and analysis using checkjob, qstat, and other tools; and parallel debugging and profiling of C and Fortran code, including logging, gdb (line-oriented debugging), ddt (GUI-based debugging) and map (GUI-based profiling) of MPI and OpenMP programs. We will issue you a temporary allocation to use for the course, or you can use your existing Flux allocations, if any.
Prerequisites
Introduction to Batch Computing on Flux or equivalent. This course assumes familiarity with the Linux command line, text editing on Linux, and a basic understanding of Flux including how to submit and track jobs.
Instructors
Dr. Charles J Antonelli
Advocacy and Research Support
LSA Information Technology
Charles is a High Performance Computing Consultant in the Advocacy and Research Support Group of LSAIT at the University of Michigan, where he is responsible for high performance computing support and education, and is an advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.
Mark Champe
Advocacy and Research Support
LSA Information Technology
Materials
- Lecture Notes (updated Feb. 2018)
- MPI Profiling with Allinea MAP
- Flux in Ten Easy Steps
- Using PBS
- Flux configuration
Course Preparation
In order to participate successfully in the workshop exercises, you must have a Flux user account, a Flux allocation (one is created for each workshop), and be enrolled in Duo. The user account allows you to log in to the cluster, create, compile, and test applications, and prepare Flux jobs for submission. The allocation allows you to submit those jobs, executing those applications in parallel on the cluster and charging their resource use against the allocation. Duo is required to help authenticate you to the cluster.
Flux user account
A single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account, you can use it for this course, you can skip to “Flux allocation” below. If not, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing, so be sure to do this at least two business days before class begins.
Flux allocation
We create an allocation for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop allocation is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Flux allocation, you can use that, though if there are any issues with that allocation, we will ask you to use the workshop allocation.
Duo Authentication
Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux.
If you need to enroll in Duo, follow the instructions at Getting Started: How to Enroll in Duo.
Please enroll in Duo before you come to class.
Laptop Preparation
You do not need to bring your own laptop to class. The classroom contains Windows computers, which require your uniqname and UMICH password to login, and that have all necessary software pre-loaded.
If you want to use a laptop for the course, you are welcome to do so: please see our web page on Preparing your laptop to use Flux. However, if there are problems connecting your laptop, you will be asked to switch to the provided computer for the class. We cannot stop to debug connection issues with personal or departmental laptops during the class.
More help
Please use our class mailing list [email protected] for questions, comments, or to seek further assistance.
